[Paper in Spanish] The suite of ideas, protocols, and software tools that has come to be known as “Ecological Niche Modeling” (ENM)—as well as those for the related “Species Distribution Modeling” (SDM)—has seen intensive exploration and research attention in recent decades. In spite of at least four syntheses, the field has grown so much in complexity that it is rather difficult to access for newcomers. Until now, accessibility to this field was achieved by in-person courses organized by universities or research centers, in some of which we have participated as instructors. However, the access to these specialized courses is limited, on one hand because they are not offered in all universities, and on the other because normally they are taught in English. To expand the access to a wider community of Spanish-speaking researchers, here we offer an entirely digital and free-of-charge course in Spanish, which was presented over 23 weeks via Internet in 2018. Although intrinsic Internet-related barriers may limit access to course materials, we have made them available in diverse formats (video, audio, pdf) in order to eliminate most of these problems.
NDM-1 carbapenemase in Acinetobacter baumannii sequence type 32 in Ecuador
May 09, 2019
Here, we describe a clinical case of Acinetobacter baumannii sequence type (ST) 32 harbouring a New Delhi metallo-β-lactamase (NDM) in Ecuador. We used multilocus sequence typing (MLST) to confirm the bacterial species and the sequence type of an A. baumannii isolate. We used synergy with the imipenem–EDTA disc method and the carbapenem inactivation method (CIM) to determine carbapenemase production; the presence of a carbapenemase gene was confirmed by PCR amplification and amplicon sequencing. Molecular characterization revealed the presence of A. baumannii ST32 harbouring the blaNDM-1 gene in Ecuador. The blaNDM-1 gene was isolated through PCR and amplified from a purified plasmid. To the best of our knowledge, this is the first report of A. baumannii ST32 harbouring the blaNDM-1 gene.
Open access solutions for biodiversity journals: Do not replace one problem with another
January 05, 2019
This publication has an story that goes beyond the paper itself. You can notice that it has the following comment at the bottom of the first page: 'This article is commented on by the publisher. To view this Publisher’s Note visit https://doi.org/10.1111/ddi.12888', which is evidence of all the background and problems behind it; among them, an open letter of disagreement of scientists due to the publisher decisions and the resignation of multiple Associate Editors from the scientific journal involved.
As I stated in this outreach pieces: 'Hopefully, the controversy about this shift [from toll to open access] will shed light on the dark side of open access, and help the public and other researchers to be aware of the waves of change that will have to be navigated if the community is to improve the current ways of scientific discovery.'
Network analysis to inform invasive species spread among lakes
December 05, 2018
Often facilitated by human-mediated pathways, aquatic invasive species are a threat to the health and biodiversity of global ecosystems. We present a novel approach incorporating survey data of watercraft movement in a social network analysis to reconstruct potential pathways of aquatic invasive species spread between lakes. As an example, we use the green alga Nitellopsis obtusa , also known as starry stonewort, an aquatic invasive species affecting the Great Lakes region in the United States and Canada. The movement of algal fragments via human-mediated pathways (i.e., watercraft) has been hypothesized as the primary driver of starry stonewort invasion. We used survey data collected at boat ramps during the 2013 and 2014 open- water seasons to describe the flow of watercraft from Lake Koronis, where N. obtusa was first detected in Minnesota, to other lakes in the state.
Sample data and training modules for cleaning biodiversity information
October 24, 2018
Large-scale biodiversity databases have become crucial information sources in many analyses in biogeography, macroecology, and conservation biology, often involving development of empirical models of species’ ecological niches and predictions of their geographic distributions. These analyses, however, can be impaired by the presence of errors, particularly as regards taxonomic identifications and accurate geographic coordinates. Here, we present a detailed data-cleaning exercise based on two contrasting datasets; we link these example data with a step-by-step guide to overcoming these problems and improving data quality for analyses based on these data. All the material for this exercise can be found in: https://kuscholarworks.ku.edu/handle/1808/26512
Evaluation of four copro-diagnostic methods for Amphimerus spp. detection in Ecuador
October 04, 2018
Amphimerus spp. is a trematode parasite from the Opistorchiidae family confirmed recently as a zoonosis colonizing the bile ducts of humans, cats, and dogs in the Chachi communities alongside the Cayapas River in the province of Esmeraldas, northwestern Ecuador. The basis of its diagnosis remains in the detection of Amphimerus spp. eggs in stool samples. Among the plethora of coproparasitological techniques available, direct smear microscopy, which is known for its poor sensitivity, is the standard recommendation for routine parasitology surveillance in Ecuador. Here, we use Amphimerus egg detection as a case study to compare different coprological techniques including the Kato-Katz, the spontaneous sedimentation technique in tube, the formalin-ether concentration, and their combination to enhance parasite detection. Our focus in Amphimerus highlights the likely scenario of misdiagnosis of this parasite in the rest of the country. We found a prevalence of 36.2% of Amphimerus in the community studied and that Kato-Katz and the combination of Kato-Katz with the spontaneous sedimentation technique in tube are effective methodologies with high sensitivities to detect the parasite.
Distributional ecology of Andes hantavirus: a macroecological approach
June 22, 2018
Hantavirus pulmonary syndrome (HPS) is an infection endemic in Chile and Argentina, caused by Andes hantavirus (ANDV). The rodent Oligoryzomys longicaudatus is suggested as the main reservoir, although several other species of Sigmodontinae are known hosts of ANDV. Here, we explore potential ANDV transmission risk to humans in southern South America, based on eco-epidemiological associations among: six rodent host species, seropositive rodents, and human HPS cases. We used ecological niche modeling and macroecological approaches to determine potential geographic distributions and assess environmental similarity among rodents and human HPS cases. Our results support a role of rodent species' distributions as a risk factor for human HPS at coarse scales, and suggest that the role of the main reservoir (O. longicaudatus) may be supported by the broader rodent host community in some areas.
Hypolobocera guayaquilensis (Decapoda: Pseudothelphusidae): a New Crab Intermediate Host of Paragonimus mexicanus in Manabí Province, Ecuador
April 18, 2018
To determine that Paragonimus sp. is actively transmitted in a tropical area of the Pacific region of Ecuador where human cases of pulmonary paragonimiasis have recently been documented, a total of 75 freshwater crabs were collected from 2 different streams in the Pedernales area of Manabí Province, Ecuador. All collected crabs were identified as Hypolobocera guayaquilensis based on morphological characteristics of the male gonopods. The hepatopancreas of each crab was examined by compressing it between 2 glass plates followed by observation under a stereomicroscope. Excysted Paragonimus metacercariae were detected in 39 (52.0%) crabs and their densities varied from 1 to 32 per infected crab. The present study is the first to confirm that the crab species H. guayaquilensis is the second intermediate host of P. mexicanus in Manabí Province, Ecuador.
Oropouche fever, an emergent disease from the Americas
December 17, 2017
Oropouche virus is the aetiological agent of Oropouche fever, a zoonotic disease mainly transmitted by midges of the species Culicoides paraensis. Although the virus was discovered in 1955, more attention has been given recently to both the virus and the disease due to outbreaks of Oropouche fever in different areas of Brazil and Peru. Serological studies in human and wild mammals have also found Oropouche virus in Argentina, Bolivia, Colombia, and Ecuador. Several mammals act as reservoirs of the disease, although the sylvatic cycle of Oropouche virus remains to be assessed properly. Oropouche fever lacks key symptoms to be differentiated from other arboviral febrile illnesses from the Americas. Sporadic cases of aseptic meningitis have also been described with good prognosis. Habitat loss can increase the likelihood of Oropouche virus emergence in the short-term in South America.
First case of New Delhi metallo-β-lactamase in Klebsiella pneumoniae from Ecuador: an update for South America
October 15, 2017
Here, we describe a clinical case of Klebsiella pneumoniae harboring New Delhi metallo-β-lactamase (NDM) plasmid in Ecuador and to present a map of reports of NDM isolates in South America. An HIV patient that has never traveled abroad developed a blood stream infection caused by K. pneumoniae ST147 harboring the NDM-1 resistant gene in a plasmid from the IncA/C group. Local circulation of NDM has also been described in other South American countries especially in Colombia and Brazil although we did not find scientific published records from other countries. We present the first evidence of autochthonous circulation of the NDM-1 resistant gene harbored by an IncA/C plasmid isolated from a K. pneumoniae ST147 in Ecuador. Efforts should be implemented to monitor and characterize the spatial and temporal distribution of NDM in Ecuador and other countries of South America.
Scorpion envenoming in Morona Santiago, Amazonian Ecuador: Molecular phylogenetics confirms involvement of the Tityus obscurus group
October 25, 2017
Scorpion sting accidents have been neglected in Ecuador since recent reports of fatal cases in the Coast region of the country. Here, we present cases of scorpion envenoming by species in the genus Tityus from rural locations in the Amazonian province of Morona Santiago, southeastern Ecuador including other two fatalities which should point out scorpionism as an important health hazard in Ecuador. With this study we are looking to emphasize the need to supply effective antivenoms against local species, which are unavailable. Moreover, we present genetic evidence of the scorpion specimens from this region and suggest the presence of a different species that was commonly described in the country.
Inferring the Ecological Niche of Toxoplasma gondii and Bartonella spp. in Wild Felids
October 17, 2017
Traditional epidemiological studies of disease in animal populations often focus on directly transmitted pathogens. One reason pathogens with complex lifecycles are understudied could be due to challenges associated with detection in vectors and the environment. Ecological niche modeling (ENM) is a methodological approach that overcomes some of the detection challenges often seen with vector or environmentally dependent pathogens. We test this approach using a unique dataset of two pathogens in wild felids across North America: Toxoplasma gondii and Bartonella spp. in bobcats (Lynx rufus) and puma (Puma concolor). We propose that ENM could be a valuable tool for enabling understanding of transmission risk, contributing to more focused prevention and control options for infectious diseases.
Amblyomma ticks and future climate: Range contraction due to climate warming
September 01, 2017
Ticks of the Amblyomma cajennense species complex are important vectors of spotted fever in Latin America. Environmental conditions determine the geographic distribution of ticks, such that climate change could influence the distribution of tick-borne diseases. This study aimed to analyze the potential geographic distribution
of A. cajennense complex ticks in a Brazil region under present-day and future climate models, assuming dispersal limitations and non-evolutionary adaptation of these tick populations to climate warming. Broad suitable areas for A. cajennense s.s. and A. sculptumwere found in present-day climate models, but suitability was reduced when models were projected to future conditions. Our exploration of future climates showed that broad areas had novel climates not existing currently in the study region, including novel extremely high temperatures. Indeed, predicted suitability in these novel conditions would lead to biologically unrealistic results and therefore incorrect forecasts of future tick- distribution. Previous studies anticipating expansions of vectors populations due to climate change should be considered with caution as they assume that model extrapolation anticipates that species would evolve rapidly for adaptation to novel climatic conditions
Forecasting distributions of an aquatic invasive species (Nitellopsis obtusa) under future climate scenarios
July 13, 2017
Emergent infectious diseases could be understood from the perspective of biological invasive species, thus, we explore current techniques of ecological niche modeling using the example of starry stonewort (Nitellopsis obtusa), an alga that has emerged as an aquatic invasive species of concern in the United States. We identify suitable areas for starry stonewort in Minnesota based on global occurrence records and present-day and future climate conditions. Our suitability maps can serve to design short-term plans for surveillance and education, while future climate models suggest a plausible reduction of starry stonewort spread in the long-term if the trends in climate warming remain.
Surveillance fatigue (fatigatio vigilantiae) during epidemics
June 14, 2017
This manuscript presents the concept of “surveillance fatigue” (fatigatiovigilantiae), to describe an epidemiological scenario of an evident underreporting of cases during overwhelming epidemics. We revised past epidemics and found that surveillance fatigue is a common pattern, thus, it may be a useful concept in modern epidemiology.
Vegetation loss and the 2016 Oropouche fever outbreak in Peru
March 15, 2017
Oropouche virus causes Oropouche fever, an arboviral disease transmitted mainly by midges of the genus Culicoides and Culex mosquitoes. Clinical presentation of Oropouche fever in humans includes fever, headache, rash, myalgia, and in rare cases spontaneous bleeding and aseptic meningitis. Landscape change has been proposed as a driver of Oropouche fever emergence. We used satellite imagery and ecological niche models to investigate the landscape epidemiology of the Oropouche fever outbreak that began in April 2016 in Cusco, Peru.
Declining prevalence of disease vectors under climate change
December 16, 2016
More than half of the world population is at risk of vector-borne diseases including dengue fever, chikungunya, zika, yellow fever, leishmaniasis, chagas disease, and malaria, with highest incidences in tropical regions. In Ecuador, vector-borne diseases are present from coastal and Amazonian regions to the Andes Mountains; however, a detailed characterization of the distribution of their vectors has never been carried out. We estimate the distribution of 14 vectors of the above vector-borne diseases under present-day and future climates. Our results consistently suggest that climate warming is likely threatening some vector species with extinction, locally or completely. These results suggest that climate change could reduce the burden of specific vector species. Other vector species are likely to shift and constrain their geographic range to the highlands in Ecuador potentially affecting novel areas and populations.
Severe pleuropulmonary paragonimiasis caused by Paragonimus mexicanus
November 05, 2016
A 30-year-old male, from a subtropical region of Ecuador, was hospitalized with a 5-year history of persistent cough with rusty brown sputum, chest pain, and progressive dyspnea. Eggs of Paragonimus spp. were observed in sputum smears, but the smears were negative for acid-fast bacilli. Molecular characterization of eggs by the internal transcribed spacer-2 regions identified them as Paragonimus mexicanus. The patient was treated with praziquantel and tested negative parasitologically for 12 months. There was clinical resolution of the cough and expectoration, but dyspnea and chest pain persisted.
Geographic distribution of leishmania species in Ecuador based on the Cytochrome B gene sequence analysis
August 31, 2016
Leishmania (Leishmania) species, LeishmaniaIn the present study, a countrywide epidemiological survey was performed to elucidate the current geographic distribution of causative species of CL in Ecuador, by using FTA card-spotted samples and smear slides as DNA sources. In Ecuador, leishmaniasis is a major public health concern reported in 21 of 24 provinces of the country, and eight mexicana, L. (L.) amazonensis, L. (L.) major-like, L. (Viannia) guyanensis, L. (V.) panamensis, L. (V.) braziliensis, L. (V.) naiffi, and L. (V.) lainsoni, have been identified as causative agents of human cutaneous (CL) and mucocutaneous leishmaniases (MCL).
Recent collections of freshwater crabs from the Pacific and Amazonian regions of Ecuador, South America
August 11, 2016
The freshwater crabs from the Provinces of Manabi and Pichincha located in the Pacific region of Ecuador collected in 2015 were identified as three species of the genus Hypolobocera of the family Pseudothelphusidae, H. aequatorialis (Ortmann, 1897), H. guayaquilensis Bott, 1967 and H. mindonensis Rodoríguez & Von Sternberg, 1998, and the specimens from the Province of Napo in the Amazonian region as two species of the genus Lindacatalina, L. latipenis (Pretzmann, 1968) and L. puyensis (Pretzmann, 1978) of the family Pseudothelphusidae, and Moreirocarcinus emarginatus (H. Milne- Edwards, 1853) of the family Trichodactylidae.
An analysis of reported cases of leishmaniasis in the southern Ecuadorian Amazon region, 1986–2012
March 03, 2015
An analysis of reported cases of cutaneous leishmaniasis (CL) was performed using the data registered in the southern Ecuadorian Amazon region during 27 years from 1986 to 2012. The cases/subjects with both the suspected CL lesions and the amastigote-positive results were recruited for the analysis.
Sand-fly fauna (Diptera, Pcychodidae, Phlebotominae) in different leishmaniasis-endemic areas of Ecuador, surveyed using a newly named Mini-Shannon trap
December 12, 2014
To study the sand fly fauna, surveys were performed at four different leishmaniasis-endemic sites in Ecuador from February 2013 to April 2014. A modified and simplified version of the conventional Shannon trap was named "mini-Shannon trap" and put to multiple uses at the different study sites in limited, forested and narrow spaces. The mini-Shannon, CDC light trap and protected human landing method were employed for sand fly collection.
Current status of Paragonimus and paragonimiasis in Ecuador.
November 10, 2014
A review of national and international publications on paragonimiasis, epidemiological records from the Ministry of Public Health, and unpublished research data, was conducted to summarise the current status of the parasite/disease. The purpose of the review is to educate physicians, policy-makers and health providers on the status of the disease and to stimulate scientific investigators to conduct further research.
Lesión cutánea esporotricoide en un paciente procedente de una región subtropical de Ecuador
August 08, 2014
Adolescentede, de 17 años nacida en Quito pero residente desde hace 8 meses en la región subtropical de Pachijal, provincia de Pichincha, Ecuador. Acudió a nuestra unidad por presentar 2 úlceras cutáneas, una en el dorso de la mano izquierda seguida de lesiones nodulares a lo largo de la mano, antebrazo y brazo, y la otra en la región axilar derecha. Refiere que las 2 lesiones aparecieron hace 3 meses.
Some freshwater crabs from South America - Ecuador
January 01, 2014
Freshwater crabs that were collected in Ecuador during the field survey for lung flukes were identified as 9 species of 2 families. The species collected from the west of the Andean Cordilleras are Hyplobocera aequatorialis (Ortmann, 1897), H. delsolari Pretzmann, 1978, H. exuca Pretzmann, 1977, and H. guayaquilensis Bott, 1967 of the family Pseudothelphusidae. The most important species from the Amazonian region is Trychodactilus faxoni.